fix: preserve gene-family stage intent and completed results
This commit is contained in:
wtx
@@ -0,0 +1,90 @@
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import json
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import subprocess
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from pathlib import Path
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PROJECT_ROOT = Path(__file__).resolve().parents[2]
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FRONTEND_PATH = PROJECT_ROOT / "apps/web/vue3/index_ml.html"
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I18N_PATH = PROJECT_ROOT / "apps/web/vue3/static/i18n_en.js"
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def _run_empty_plan_branch(tmp_path: Path, plan_data: dict) -> dict:
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frontend = FRONTEND_PATH.read_text(encoding="utf-8")
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start = frontend.index("const plan = planData.plan;")
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end = frontend.index("// 显示智能规划结果", start)
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branch = frontend[start:end]
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script = tmp_path / "empty-plan-branch.cjs"
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script.write_text(
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"const planData=" + json.dumps(plan_data, ensure_ascii=False) + ";"
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"const events={messages:[],filters:[],refreshes:[]};"
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"const t=value=>value;"
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"const getStageLabel=id=>({genome_prepare:'0️⃣ Genome Prepare',ppi:'PPI分析'}[id]||id);"
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"const setResultStageFilter=id=>events.filters.push(id);"
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"const refreshResults=async(jobId,id)=>events.refreshes.push([jobId,id]);"
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"const addAgentMessage=(role,message,meta)=>events.messages.push({role,message,meta});"
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"const jobInfo={job_id:'job-test'};"
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"const nlLoading={value:true};const nlInput={value:'request'};"
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"async function run(){" + branch + "}"
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"run().then(()=>process.stdout.write(JSON.stringify(events)));",
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encoding="utf-8",
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)
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completed = subprocess.run(
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["/usr/bin/node", str(script)],
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text=True,
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capture_output=True,
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check=False,
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)
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assert completed.returncode == 0, completed.stderr
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return json.loads(completed.stdout)
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def test_completed_full_workflow_does_not_masquerade_as_genome_prepare(tmp_path: Path) -> None:
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requested = ["phylogeny", "motif", "domain", "structure", "combo", "promoter"]
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result = _run_empty_plan_branch(
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tmp_path,
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{
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"success": True,
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"plan": {
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"stages": [],
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"all_stages": requested,
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"description": "所有阶段已完成",
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},
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"completed_stages": [*requested, "genome_prepare"],
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},
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)
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assert result["filters"] == []
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assert result["refreshes"] == []
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assert [item["message"] for item in result["messages"]] == [
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"当前请求中的分析阶段均已有同一分析范围的有效结果，无需重复执行。"
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]
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def test_completed_single_stage_keeps_stage_specific_result_handoff(tmp_path: Path) -> None:
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result = _run_empty_plan_branch(
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tmp_path,
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{
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"success": True,
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"plan": {
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"stages": [],
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"all_stages": ["ppi"],
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"description": "所有阶段已完成",
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},
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"completed_stages": ["ppi"],
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},
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)
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assert result["filters"] == ["ppi"]
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assert result["refreshes"] == [["job-test", "ppi"]]
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assert [item["message"] for item in result["messages"]] == [
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"PPI分析 已有同一分析范围的有效结果，无需重复执行。"
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]
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def test_generic_completed_plan_label_has_english_translation() -> None:
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translations = I18N_PATH.read_text(encoding="utf-8")
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assert (
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'"当前请求中的分析阶段均已有同一分析范围的有效结果，无需重复执行。": '
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'"All analysis stages in the current request already have valid results for the same analysis scope. No need to re-execute."'
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) in translations
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@@ -0,0 +1,124 @@
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from pathlib import Path
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_ORIGINAL_PATH_MKDIR = Path.mkdir
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def _ignore_broken_remote_mount_mkdir(path: Path, *args, **kwargs):
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if path.is_symlink() and not path.exists():
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return None
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return _ORIGINAL_PATH_MKDIR(path, *args, **kwargs)
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Path.mkdir = _ignore_broken_remote_mount_mkdir
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try:
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from apps.web.vue3 import main as web_main
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finally:
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Path.mkdir = _ORIGINAL_PATH_MKDIR
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def _full_plan_inputs():
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stage_ids = ["identify", *web_main.FULL_GENE_FAMILY_WORKFLOW_STAGES]
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details = [web_main._stage_detail_defaults(stage_id) for stage_id in stage_ids]
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params = {
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"targetSpecies": ["Ft"],
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"referenceSpecies": ["At"],
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"geneFamily": "SPL",
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}
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return stage_ids, details, params
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def test_full_workflow_normalization_respects_intent_stage_exclusions():
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stage_ids, details, params = _full_plan_inputs()
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for excluded_stage in ("kaks", "karyotype"):
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authorized = [stage for stage in stage_ids if stage != excluded_stage]
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normalized, _ = web_main._normalize_full_gene_family_workflow_plan(
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message=f"执行基因家族分析，但是不要执行{excluded_stage}",
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stage_ids=stage_ids,
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stages_detail=details,
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plan_params=dict(params),
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plan_prefix="Ft.SPL",
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authorized_stage_ids=authorized,
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)
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assert excluded_stage not in normalized
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assert set(normalized) == set(authorized)
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def test_full_workflow_normalization_keeps_full_intent_and_required_dependencies():
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stage_ids, details, params = _full_plan_inputs()
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normalized, _ = web_main._normalize_full_gene_family_workflow_plan(
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message="执行基因家族分析",
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stage_ids=stage_ids,
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stages_detail=details,
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plan_params=dict(params),
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plan_prefix="Ft.SPL",
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authorized_stage_ids=stage_ids,
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)
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assert normalized == stage_ids
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assert normalized.index("ppi") < normalized.index("kaks")
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normalized_without_supplied_intent, _ = web_main._normalize_full_gene_family_workflow_plan(
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message="执行基因家族分析",
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stage_ids=stage_ids,
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stages_detail=details,
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plan_params=dict(params),
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plan_prefix="Ft.SPL",
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authorized_stage_ids=[],
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)
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assert normalized_without_supplied_intent == stage_ids
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dependency_stages = ["identify", "synteny", "karyotype"]
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dependency_details = [web_main._stage_detail_defaults(stage) for stage in dependency_stages]
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normalized_dependencies, _ = web_main._normalize_full_gene_family_workflow_plan(
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message="执行核型分析",
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stage_ids=dependency_stages,
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stages_detail=dependency_details,
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plan_params=dict(params),
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plan_prefix="Ft.SPL",
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authorized_stage_ids=dependency_stages,
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)
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assert normalized_dependencies == dependency_stages
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def test_contextual_full_workflow_uses_request_intent_as_stage_authority():
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stage_ids, _, params = _full_plan_inputs()
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authorized = [stage for stage in stage_ids if stage != "kaks"]
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request = web_main.AgentPlanRequest(
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message="执行基因家族分析，但是不要执行kaks分析",
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prefix="Ft.SPL",
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intent={"stages": authorized, "params": params},
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)
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contextual_request = {
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"family": "SPL",
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"prefix": "Ft.SPL",
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"stages": stage_ids,
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"targetSpecies": ["Ft"],
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"referenceSpecies": ["At"],
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"comparativeSpecies": [],
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"scopeMode": "target_plus_reference",
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"requiresConfirmedSubfamily": True,
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"skipSubfamilyLabels": False,
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"subfamilyState": {"by_species": {"Ft": {"status": "confirmed"}}},
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"contextGate": {"status": "ready", "issues": []},
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}
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response = web_main._build_contextual_gene_family_plan_response(
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request,
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"test_intent_stage_authority",
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contextual_request,
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)
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assert "kaks" not in response["plan"]["stages"]
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def test_llm_plan_normalization_calls_keep_original_intent_stage_authority():
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source = (web_main.PROJECT_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")
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start = source.index("full_workflow_normalized = False")
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end = source.index("stage_ids, stages_detail = _apply_standard_combo_panel_plan", start)
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normalization_block = source[start:end]
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assert "plan_authorized_stage_ids = authoritative_intent_stage_ids or" in source
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assert normalization_block.count("authorized_stage_ids=plan_authorized_stage_ids") == 2
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@@ -0,0 +1,144 @@
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import asyncio
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import json
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from types import SimpleNamespace
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from gfa_core.mas.agents.base import AgentMessage, AgentState
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from gfa_core.mas.agents.intent_v2 import IntentAgentV2
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from gfa_core.mas.core.fast_intent import fast_intent_recognition
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from gfa_core.mas.utils.intent_parser import CORE_STAGES, parse_intent_from_query
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def test_complete_gene_family_workflow_excludes_explicitly_negated_ppi():
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intent = parse_intent_from_query("执行完整流程，但不执行PPI")
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assert intent["stages"] == [stage for stage in CORE_STAGES if stage != "ppi"]
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def test_symbolic_minus_excludes_stage_from_complete_workflow():
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intent = parse_intent_from_query("完整流程 - PPI")
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assert intent["stages"] == [stage for stage in CORE_STAGES if stage != "ppi"]
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def test_mixed_positive_and_negative_stages_keep_only_positive_targets():
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intent = parse_intent_from_query("做系统发育和Motif，不要做结构域分析")
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assert intent["stages"] == ["phylogeny", "motif"]
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def test_positive_ppi_and_kaks_request_is_unchanged():
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intent = parse_intent_from_query("执行PPI和KaKs分析")
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assert intent["stages"] == ["kaks", "ppi"]
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def test_generic_rnaseq_workflow_excludes_wgcna_target():
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intent = parse_intent_from_query("执行RNA-seq分析，但不要WGCNA")
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assert intent["stages"] == [
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"rnaseq_de",
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"rnaseq_go_enrich",
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"rnaseq_kegg_enrich",
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"rnaseq_fgsea",
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"rnaseq_candidate_family",
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]
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def test_pure_negative_request_never_becomes_positive_in_rule_fallbacks():
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parsed = parse_intent_from_query("不要执行PPI")
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fallback = IntentAgentV2(None)._fallback_recognition("不要执行PPI")
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fast = fast_intent_recognition("不要执行PPI")
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assert parsed["stages"] == []
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assert parsed["need_clarify"] is True
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assert fallback["stages"] == []
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assert fallback["needs_clarification"] is True
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assert fast is None
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def test_model_output_cannot_reintroduce_a_negated_stage():
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class _PpiLLM:
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async def acall(self, *_args, **_kwargs):
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return SimpleNamespace(
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content=json.dumps(
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{
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"gene_family": "SPL",
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"species": "Ft",
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"stages": ["ppi"],
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"primary_stage": "ppi",
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"description": "执行PPI分析",
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"requirements": [],
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"confidence": 0.9,
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}
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)
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)
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state = AgentState(session_id="negated-stage", job_id="job-negated-stage")
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message = AgentMessage(
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sender="router",
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receiver="intent_v2",
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message_type="recognize_intent",
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payload={"query": "不要执行PPI"},
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)
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returned = asyncio.run(IntentAgentV2(_PpiLLM()).execute(state, message))
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intent = returned.results["results"]["intent"]
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assert intent["stages"] == []
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assert intent["needs_clarification"] is True
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def test_dependency_completion_can_restore_required_non_target_stage():
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class _ForbiddenLLM:
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async def acall(self, *_args, **_kwargs):
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raise AssertionError("deterministic intent must not call the LLM")
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state = AgentState(session_id="dependency", job_id="job-dependency")
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message = AgentMessage(
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sender="router",
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receiver="intent_v2",
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message_type="recognize_intent",
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payload={"query": "执行核型分析，不单独执行种内共线性"},
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)
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returned = asyncio.run(IntentAgentV2(_ForbiddenLLM()).execute(state, message))
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intent = returned.results["results"]["intent"]
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assert intent["primary_stage"] == "karyotype"
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assert intent["stages"] == ["identify", "synteny", "karyotype"]
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def test_completed_subfamily_context_does_not_override_current_stage_negation():
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class _ForbiddenLLM:
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async def acall(self, *_args, **_kwargs):
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raise AssertionError("deterministic intent must not call the LLM")
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state = AgentState(session_id="context-negation", job_id="job-context-negation")
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message = AgentMessage(
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sender="router",
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receiver="intent_v2",
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message_type="recognize_intent",
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payload={
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"query": (
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"帮我执行Ft的基因家族分析，但是不要执行kaks分析\n"
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"已确认上下文：基因家族 SPL；目标物种 Ft；参考物种 At；"
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"当前 job 的 subfamily_confirm 已成功完成，家族成员和亚家族分类表已确认。"
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),
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},
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)
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returned = asyncio.run(IntentAgentV2(_ForbiddenLLM()).execute(state, message))
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intent = returned.results["results"]["intent"]
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assert intent["gene_family"] == "SPL"
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assert intent["species"] == "Ft"
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assert "ppi" in intent["stages"]
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assert "kaks" not in intent["stages"]
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assert "reference_classification" not in intent["stages"]
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def test_subfamily_classification_bypasses_generic_stage_negation():
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intent = parse_intent_from_query("执行亚家族分类，不要结构域分析")
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assert "reference_classification" in intent["stages"]
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assert "domain" in intent["stages"]
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@@ -2,6 +2,7 @@ from __future__ import annotations
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import hashlib
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import json
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import os
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def _write_ft_technical_reference_manifest(final_dir, stage, *, status="success"):
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@@ -34,6 +35,50 @@ def _write_ft_technical_reference_manifest(final_dir, stage, *, status="success"
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return manifest
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def _write_regular_gene_family_manifest(
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final_dir,
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stage,
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*,
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scope_id="SPL.target-Ft.ref-At.target_plus_reference",
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route="multi_species",
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references=None,
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member_set_id="",
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filename="",
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with_artifact=True,
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):
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references = ["At"] if references is None else list(references)
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member_set_id = member_set_id or f"{scope_id}:{route}:all_members"
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artifact = final_dir / f"Ft.SPL.{stage}.result.tsv"
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if with_artifact:
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artifact.write_text(f"{stage}\tresult\n", encoding="utf-8")
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manifest = final_dir / (filename or f"Ft.SPL.scoped.{stage}.manifest.json")
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manifest.write_text(
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json.dumps(
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{
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"manifest_version": "1.0",
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"stage": stage,
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"status": "success",
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"prefix": "Ft.SPL",
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"scope_id": scope_id,
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"scope_mode": "target_plus_reference" if references else "target_only",
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"analysis_route": route,
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"member_set_id": member_set_id,
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"family": "SPL",
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"target_species": ["Ft"],
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"reference_species": references,
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"artifacts": (
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{"result": {"path": f"final/{artifact.name}", "type": "tsv"}}
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if with_artifact
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else {"result": {"path": "final/missing.tsv", "type": "tsv"}}
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),
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},
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ensure_ascii=False,
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),
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encoding="utf-8",
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)
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return manifest
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def _confirmed_contextual_ppi_fixture(web_main, workspace_root, job_id, intent_params):
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from types import SimpleNamespace
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@@ -416,6 +461,179 @@ def test_identity_completed_stages_force_rerun_keeps_technical_stages_pending(tm
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assert completed == []
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def test_post_confirm_plan_recovers_regular_manifest_identity(tmp_path, monkeypatch):
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from apps.web.vue3 import main as web_main
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workspace_root = tmp_path / "workspace"
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final_dir = workspace_root / "job_regular_recovery" / "final"
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final_dir.mkdir(parents=True)
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confirm = final_dir / "Ft.SPL.subfamily_confirm.manifest.json"
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confirm.write_text('{"stage":"subfamily_confirm","status":"success","prefix":"Ft.SPL"}', encoding="utf-8")
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manifest = _write_regular_gene_family_manifest(final_dir, "phylogeny")
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os.utime(confirm, (1, 1))
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os.utime(manifest, (2, 2))
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monkeypatch.setattr(web_main, "WORKSPACE_ROOT", workspace_root)
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||||
|
||||
scope_id = "SPL.target-Ft.ref-At.target_plus_reference"
|
||||
plan_params = {
|
||||
"prefix": "Ft.SPL",
|
||||
"geneFamily": "SPL",
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"workflowPhase": "post_subfamily_confirm",
|
||||
"requiresConfirmedSubfamily": True,
|
||||
}
|
||||
stage_params = {
|
||||
**plan_params,
|
||||
"scopeMode": "target_plus_reference",
|
||||
"analysisRoute": "multi_species",
|
||||
"memberSetId": f"{scope_id}:confirmed_subfamily:all_members",
|
||||
}
|
||||
|
||||
completed = web_main._identity_completed_stages_for_plan(
|
||||
"job_regular_recovery",
|
||||
["phylogeny"],
|
||||
plan_params,
|
||||
[{"id": "phylogeny", "params": stage_params}],
|
||||
request_prefix="Ft.SPL",
|
||||
)
|
||||
|
||||
assert completed == ["phylogeny"]
|
||||
|
||||
|
||||
def test_post_confirm_plan_tries_next_manifest_after_incomplete_alias(tmp_path, monkeypatch):
|
||||
from apps.web.vue3 import main as web_main
|
||||
|
||||
workspace_root = tmp_path / "workspace"
|
||||
final_dir = workspace_root / "job_regular_alias" / "final"
|
||||
final_dir.mkdir(parents=True)
|
||||
confirm = final_dir / "Ft.SPL.subfamily_confirm.manifest.json"
|
||||
confirm.write_text('{"stage":"subfamily_confirm","status":"success","prefix":"Ft.SPL"}', encoding="utf-8")
|
||||
canonical = _write_regular_gene_family_manifest(
|
||||
final_dir,
|
||||
"synteny",
|
||||
route="single_species",
|
||||
filename="Ft.SPL.scoped.synteny.manifest.json",
|
||||
)
|
||||
alias = _write_regular_gene_family_manifest(
|
||||
final_dir,
|
||||
"synteny",
|
||||
route="single_species",
|
||||
filename="Ft.SPL.synteny.manifest.json",
|
||||
with_artifact=False,
|
||||
)
|
||||
alias_payload = json.loads(alias.read_text(encoding="utf-8"))
|
||||
for key in ("scope_id", "scope_mode", "analysis_route", "member_set_id"):
|
||||
alias_payload.pop(key, None)
|
||||
alias.write_text(json.dumps(alias_payload), encoding="utf-8")
|
||||
os.utime(confirm, (1, 1))
|
||||
os.utime(canonical, (2, 2))
|
||||
os.utime(alias, (3, 3))
|
||||
monkeypatch.setattr(web_main, "WORKSPACE_ROOT", workspace_root)
|
||||
|
||||
target_scope = "SPL.target-Ft.target_only"
|
||||
plan_params = {
|
||||
"prefix": "Ft.SPL",
|
||||
"geneFamily": "SPL",
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"workflowPhase": "post_subfamily_confirm",
|
||||
"requiresConfirmedSubfamily": True,
|
||||
}
|
||||
stage_params = {
|
||||
**plan_params,
|
||||
"referenceSpecies": [],
|
||||
"scopeMode": "target_only",
|
||||
"analysisRoute": "single_species",
|
||||
"memberSetId": f"{target_scope}:confirmed_subfamily:all_members",
|
||||
}
|
||||
|
||||
completed = web_main._identity_completed_stages_for_plan(
|
||||
"job_regular_alias",
|
||||
["synteny"],
|
||||
plan_params,
|
||||
[{"id": "synteny", "params": stage_params}],
|
||||
request_prefix="Ft.SPL",
|
||||
)
|
||||
|
||||
assert completed == ["synteny"]
|
||||
|
||||
|
||||
def test_post_confirm_plan_rejects_result_older_than_confirmation(tmp_path, monkeypatch):
|
||||
from apps.web.vue3 import main as web_main
|
||||
|
||||
workspace_root = tmp_path / "workspace"
|
||||
final_dir = workspace_root / "job_regular_stale" / "final"
|
||||
final_dir.mkdir(parents=True)
|
||||
manifest = _write_regular_gene_family_manifest(final_dir, "phylogeny")
|
||||
confirm = final_dir / "Ft.SPL.subfamily_confirm.manifest.json"
|
||||
confirm.write_text('{"stage":"subfamily_confirm","status":"success","prefix":"Ft.SPL"}', encoding="utf-8")
|
||||
os.utime(manifest, (1, 1))
|
||||
os.utime(confirm, (2, 2))
|
||||
monkeypatch.setattr(web_main, "WORKSPACE_ROOT", workspace_root)
|
||||
|
||||
scope_id = "SPL.target-Ft.ref-At.target_plus_reference"
|
||||
plan_params = {
|
||||
"prefix": "Ft.SPL",
|
||||
"geneFamily": "SPL",
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"workflowPhase": "post_subfamily_confirm",
|
||||
"requiresConfirmedSubfamily": True,
|
||||
}
|
||||
stage_params = {
|
||||
**plan_params,
|
||||
"scopeMode": "target_plus_reference",
|
||||
"analysisRoute": "multi_species",
|
||||
"memberSetId": f"{scope_id}:confirmed_subfamily:all_members",
|
||||
}
|
||||
|
||||
completed = web_main._identity_completed_stages_for_plan(
|
||||
"job_regular_stale",
|
||||
["phylogeny"],
|
||||
plan_params,
|
||||
[{"id": "phylogeny", "params": stage_params}],
|
||||
request_prefix="Ft.SPL",
|
||||
)
|
||||
|
||||
assert completed == []
|
||||
|
||||
|
||||
def test_post_confirm_kaks_inherits_completed_shared_ppi_reference(tmp_path, monkeypatch):
|
||||
from apps.web.vue3 import main as web_main
|
||||
|
||||
workspace_root = tmp_path / "workspace"
|
||||
final_dir = workspace_root / "job_contextual_kaks" / "final"
|
||||
final_dir.mkdir(parents=True)
|
||||
_write_ft_technical_reference_manifest(final_dir, "kaks")
|
||||
monkeypatch.setattr(web_main, "WORKSPACE_ROOT", workspace_root)
|
||||
|
||||
plan_params = {
|
||||
"prefix": "Ft.SPL",
|
||||
"geneFamily": "SPL",
|
||||
"targetSpecies": ["Ft"],
|
||||
"referenceSpecies": ["At"],
|
||||
"workflowPhase": "post_subfamily_confirm",
|
||||
"requiresConfirmedSubfamily": True,
|
||||
}
|
||||
stage_params = {
|
||||
**plan_params,
|
||||
"scopeMode": "target_plus_reference",
|
||||
"analysisRoute": "multi_species",
|
||||
"memberSetId": "SPL.target-Ft.ref-At.target_plus_reference:confirmed_subfamily:all_members",
|
||||
}
|
||||
|
||||
completed = web_main._identity_completed_stages_for_plan(
|
||||
"job_contextual_kaks",
|
||||
["kaks"],
|
||||
plan_params,
|
||||
[{"id": "kaks", "params": stage_params}],
|
||||
request_prefix="Ft.SPL",
|
||||
)
|
||||
|
||||
assert completed == ["kaks"]
|
||||
|
||||
|
||||
|
||||
|
||||
def test_contextual_plan_returns_only_pending_stages(tmp_path, monkeypatch):
|
||||
|
||||
Reference in New Issue
Block a user